SMTL ID : 3gm6.1

Structure of the Thioalkalivibrio nitratireducens cytochrome c nitrite reductase in complex with phosphate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-hexamer

Ligands

48 x HEC: HEME C(Covalent)

HEC.1: 27 residues within 4Å: Chain A: H.113, A.114, E.115, P.116, D.125, H.126, V.129, R.131, A.132, A.179, A.180, C.184, C.187, K.188, R.242, Q.298, C.299, H.300, V.301, Y.303, C.305, F.327, H.361, A.484, N.486 Ligands: HEC.3, PO4.9 21 PLIP interactions: 21 interactions with chain A, Hydrophobic interactions: A:V.129, A:A.132, A:V.301, A:Y.303, A:Y.303, A:F.327 Hydrogen bonds: A:A.114, A:A.484, A:N.486 Water bridges: A:K.90, A:K.90, A:H.113, A:H.113, A:R.131 Salt bridges: A:K.90, A:H.113, A:R.131, A:H.361 pi-Stacking: A:Y.303, A:H.361 pi-Cation interactions: A:H.126 HEC.2: 21 residues within 4Å: Chain A: C.66, H.70, Q.73, F.74, F.77, L.225, N.226, C.227, M.229, C.230, H.231, A.290, S.292, M.295, M.384, K.386, Y.395, T.396, H.398 Ligands: HEC.3, HEC.7 12 PLIP interactions: 12 interactions with chain A, Hydrophobic interactions: A:H.70, A:Q.73, A:Q.73, A:L.225, A:A.290, A:T.396 Hydrogen bonds: A:Q.73, A:T.396, A:T.396 Salt bridges: A:K.386 Metal complexes: A:H.231, A:H.398 HEC.3: 26 residues within 4Å: Chain A: R.81, S.84, P.116, R.117, S.118, H.119, F.121, M.122, D.125, C.187, K.188, L.225, M.229, S.292, C.296, Q.298, C.299, H.300, C.379, H.383, M.384, Q.400, R.401 Ligands: HEC.1, HEC.2, HEC.4 9 PLIP interactions: 9 interactions with chain A, Hydrophobic interactions: A:P.116, A:L.225, A:H.383 Hydrogen bonds: A:P.116, A:R.117, A:F.121, A:D.125 Metal complexes: A:H.119, A:H.300 HEC.4: 24 residues within 4Å: Chain A: P.116, N.293, C.296, H.300, E.363, A.364, F.367, H.372, V.377, A.378, C.379, C.382, H.383, T.402, P.403, R.404, I.427, K.431, N.486, S.487, F.490, H.491 Ligands: HEC.3, HEC.5 20 PLIP interactions: 20 interactions with chain A, Hydrophobic interactions: A:H.300, A:E.363, A:E.363, A:F.367, A:H.372, A:V.377, A:P.403, A:I.427, A:N.486, A:F.490, A:F.490 Hydrogen bonds: A:T.402 Water bridges: A:R.404, A:R.404, A:N.486, A:N.486 Salt bridges: A:R.404, A:K.431 Metal complexes: A:H.383, A:H.491 HEC.5: 20 residues within 4Å: Chain A: V.371, H.372, N.375, V.377, D.381, C.382, P.403, A.410, C.411, C.414, H.415, W.418, A.423, I.427, F.490, P.493 Chain C: N.141, W.142, Q.143 Ligands: HEC.4 11 PLIP interactions: 8 interactions with chain A, 3 interactions with chain C, Hydrophobic interactions: A:V.371, A:V.377, A:P.403, A:W.418, A:I.427, A:F.490, C:Q.143 Metal complexes: A:H.372, A:H.415 Hydrogen bonds: C:W.142 Water bridges: C:Q.143 HEC.6: 23 residues within 4Å: Chain A: C.14, F.15, H.18, I.21, H.25, V.33, N.34, C.35, H.37, C.38, H.39, T.59, I.193, L.194, F.228, P.233, H.234, R.239, F.274, R.276, R.282 Ligands: HEC.7, HEC.8 17 PLIP interactions: 17 interactions with chain A, Hydrophobic interactions: A:F.15, A:I.21, A:V.33, A:T.59, A:I.193, A:L.194, A:F.228, A:P.233, A:P.233, A:F.274 Water bridges: A:H.234 Salt bridges: A:R.239, A:R.276, A:R.282, A:R.282 Metal complexes: A:H.39, A:H.234 HEC.7: 20 residues within 4Å: Chain A: K.29, H.30, V.33, H.37, A.65, C.66, T.68, C.69, H.70, C.227, F.228, H.231, P.233, A.236 Chain B: H.37, T.68, C.69 Ligands: HEC.2, HEC.6, HEC.19 11 PLIP interactions: 10 interactions with chain A, 1 interactions with chain B, Hydrophobic interactions: A:K.29, A:K.29, A:V.33, A:T.68, A:H.231 Water bridges: A:K.29, B:N.5 Salt bridges: A:K.29, A:K.29 Metal complexes: A:H.30, A:H.70 HEC.8: 22 residues within 4Å: Chain A: V.9, Q.13, C.14, C.17, H.18, C.35, H.39, A.41, H.44, V.45, A.48, S.49, S.50, R.52, M.53, R.56, P.57, T.59, L.194, R.276, G.277 Ligands: HEC.6 14 PLIP interactions: 14 interactions with chain A, Hydrophobic interactions: A:V.9, A:A.41, A:V.45, A:M.53, A:P.57 Hydrogen bonds: A:G.277 Water bridges: A:R.276, A:R.276 Salt bridges: A:R.56, A:R.276, A:R.276 pi-Stacking: A:H.18 Metal complexes: A:H.18, A:H.44 HEC.13: 25 residues within 4Å: Chain B: H.113, A.114, E.115, P.116, D.125, H.126, V.129, R.131, A.179, A.180, C.184, C.187, K.188, R.242, Q.298, C.299, H.300, V.301, Y.303, C.305, F.327, H.361, N.486 Ligands: HEC.15, PO4.21 19 PLIP interactions: 19 interactions with chain B, Hydrophobic interactions: B:V.129, B:V.301, B:Y.303, B:Y.303, B:F.327 Hydrogen bonds: B:A.114, B:A.484, B:N.486 Water bridges: B:H.113, B:H.113, B:A.114, B:R.131 Salt bridges: B:K.90, B:H.113, B:R.131, B:H.361 pi-Stacking: B:Y.303, B:H.361 pi-Cation interactions: B:H.126 HEC.14: 20 residues within 4Å: Chain B: C.66, H.70, Q.73, F.74, F.77, L.225, N.226, C.227, M.229, C.230, H.231, A.290, S.292, M.295, M.384, Y.395, T.396, H.398 Ligands: HEC.15, HEC.19 11 PLIP interactions: 11 interactions with chain B, Hydrophobic interactions: B:H.70, B:Q.73, B:Q.73, B:L.225, B:A.290, B:T.396 Hydrogen bonds: B:Q.73, B:T.396 Salt bridges: B:K.386 Metal complexes: B:H.231, B:H.398 HEC.15: 27 residues within 4Å: Chain B: R.81, S.84, P.116, R.117, S.118, H.119, F.121, M.122, D.125, C.187, K.188, L.225, M.229, S.292, M.295, C.296, Q.298, C.299, H.300, C.379, H.383, M.384, Q.400, R.401 Ligands: HEC.13, HEC.14, HEC.16 12 PLIP interactions: 12 interactions with chain B, Hydrophobic interactions: B:P.116, B:K.188, B:L.225, B:H.383 Hydrogen bonds: B:R.117, B:F.121 Water bridges: B:S.84, B:S.118, B:H.126, B:Q.400 Metal complexes: B:H.119, B:H.300 HEC.16: 23 residues within 4Å: Chain B: N.293, C.296, H.300, E.363, A.364, F.367, H.372, V.377, A.378, C.379, C.382, H.383, T.402, P.403, R.404, I.427, K.431, N.486, S.487, F.490, H.491 Ligands: HEC.15, HEC.17 22 PLIP interactions: 22 interactions with chain B, Hydrophobic interactions: B:H.300, B:E.363, B:E.363, B:F.367, B:H.372, B:V.377, B:P.403, B:I.427, B:N.486, B:F.490, B:F.490 Hydrogen bonds: B:T.402 Water bridges: B:S.84, B:R.404, B:R.404, B:K.431, B:N.486, B:N.486 Salt bridges: B:R.404, B:K.431 Metal complexes: B:H.383, B:H.491 HEC.17: 20 residues within 4Å: Chain B: V.371, H.372, N.375, V.377, D.381, C.382, P.403, A.410, C.411, C.414, H.415, W.418, A.423, I.427, F.490, P.493 Chain F: N.141, W.142, Q.143 Ligands: HEC.16 13 PLIP interactions: 9 interactions with chain B, 4 interactions with chain F, Hydrophobic interactions: B:V.371, B:N.375, B:V.377, B:P.403, B:W.418, B:I.427, B:F.490, F:Q.143 Metal complexes: B:H.372, B:H.415 Hydrogen bonds: F:W.142, F:Q.143 Water bridges: F:Q.143 HEC.18: 24 residues within 4Å: Chain B: A.11, C.14, F.15, H.18, I.21, H.25, V.33, N.34, C.35, H.37, C.38, H.39, T.59, I.193, L.194, F.228, P.233, H.234, R.239, F.274, R.276, R.282 Ligands: HEC.19, HEC.20 18 PLIP interactions: 18 interactions with chain B, Hydrophobic interactions: B:A.11, B:F.15, B:I.21, B:I.21, B:V.33, B:T.59, B:I.193, B:L.194, B:F.228, B:P.233, B:F.274 Water bridges: B:H.234 Salt bridges: B:R.239, B:R.276, B:R.282, B:R.282 Metal complexes: B:H.39, B:H.234 HEC.19: 19 residues within 4Å: Chain A: H.37, T.68, C.69 Chain B: K.29, H.30, V.33, H.37, A.65, C.66, C.69, H.70, C.227, F.228, H.231, P.233, A.236 Ligands: HEC.7, HEC.14, HEC.18 7 PLIP interactions: 7 interactions with chain B, Hydrophobic interactions: B:K.29, B:V.33, B:H.231 Salt bridges: B:K.29, B:K.29 Metal complexes: B:H.30, B:H.70 HEC.20: 23 residues within 4Å: Chain B: Q.13, C.14, C.17, H.18, C.35, H.39, A.41, H.44, V.45, A.48, S.49, S.50, R.51, R.52, M.53, R.56, P.57, T.59, L.194, Q.275, R.276, G.277 Ligands: HEC.18 14 PLIP interactions: 14 interactions with chain B, Hydrophobic interactions: B:A.41, B:V.45, B:M.53, B:P.57 Water bridges: B:H.18, B:Q.275, B:R.276, B:R.276, B:R.278, B:R.278 Salt bridges: B:R.56, B:R.276 Metal complexes: B:H.18, B:H.44 HEC.25: 27 residues within 4Å: Chain C: H.113, A.114, E.115, P.116, D.125, H.126, V.129, R.131, A.132, A.179, A.180, C.184, C.187, K.188, R.242, Q.298, C.299, H.300, V.301, Y.303, C.305, F.327, H.361, A.484, N.486 Ligands: HEC.27, PO4.33 21 PLIP interactions: 21 interactions with chain C, Hydrophobic interactions: C:V.129, C:A.132, C:V.301, C:Y.303, C:Y.303, C:F.327 Hydrogen bonds: C:A.114, C:A.484, C:N.486 Water bridges: C:K.90, C:K.90, C:H.113, C:H.113, C:R.131 Salt bridges: C:K.90, C:H.113, C:R.131, C:H.361 pi-Stacking: C:Y.303, C:H.361 pi-Cation interactions: C:H.126 HEC.26: 21 residues within 4Å: Chain C: C.66, H.70, Q.73, F.74, F.77, L.225, N.226, C.227, M.229, C.230, H.231, A.290, S.292, M.295, M.384, K.386, Y.395, T.396, H.398 Ligands: HEC.27, HEC.31 11 PLIP interactions: 11 interactions with chain C, Hydrophobic interactions: C:H.70, C:Q.73, C:Q.73, C:L.225, C:A.290, C:T.396 Hydrogen bonds: C:Q.73, C:T.396 Salt bridges: C:K.386 Metal complexes: C:H.231, C:H.398 HEC.27: 26 residues within 4Å: Chain C: R.81, S.84, P.116, R.117, S.118, H.119, F.121, M.122, D.125, C.187, K.188, L.225, M.229, S.292, C.296, Q.298, C.299, H.300, C.379, H.383, M.384, Q.400, R.401 Ligands: HEC.25, HEC.26, HEC.28 8 PLIP interactions: 8 interactions with chain C, Hydrophobic interactions: C:P.116, C:L.225, C:H.383 Hydrogen bonds: C:P.116, C:R.117, C:F.121 Metal complexes: C:H.119, C:H.300 HEC.28: 24 residues within 4Å: Chain C: P.116, N.293, C.296, H.300, E.363, A.364, F.367, H.372, V.377, A.378, C.379, C.382, H.383, T.402, P.403, R.404, I.427, K.431, N.486, S.487, F.490, H.491 Ligands: HEC.27, HEC.29 20 PLIP interactions: 20 interactions with chain C, Hydrophobic interactions: C:H.300, C:E.363, C:E.363, C:F.367, C:H.372, C:V.377, C:P.403, C:I.427, C:N.486, C:F.490, C:F.490 Hydrogen bonds: C:T.402 Water bridges: C:R.404, C:R.404, C:N.486, C:N.486 Salt bridges: C:R.404, C:K.431 Metal complexes: C:H.383, C:H.491 HEC.29: 20 residues within 4Å: Chain C: V.371, H.372, N.375, V.377, D.381, C.382, P.403, A.410, C.411, C.414, H.415, W.418, A.423, I.427, F.490, P.493 Chain E: N.141, W.142, Q.143 Ligands: HEC.28 11 PLIP interactions: 8 interactions with chain C, 3 interactions with chain E, Hydrophobic interactions: C:V.371, C:V.377, C:P.403, C:W.418, C:I.427, C:F.490, E:Q.143 Metal complexes: C:H.372, C:H.415 Hydrogen bonds: E:W.142 Water bridges: E:Q.143 HEC.30: 23 residues within 4Å: Chain C: C.14, F.15, H.18, I.21, H.25, V.33, N.34, C.35, H.37, C.38, H.39, T.59, I.193, L.194, F.228, P.233, H.234, R.239, F.274, R.276, R.282 Ligands: HEC.31, HEC.32 17 PLIP interactions: 17 interactions with chain C, Hydrophobic interactions: C:F.15, C:I.21, C:V.33, C:T.59, C:I.193, C:L.194, C:F.228, C:P.233, C:P.233, C:F.274 Water bridges: C:H.234 Salt bridges: C:R.239, C:R.276, C:R.282, C:R.282 Metal complexes: C:H.39, C:H.234 HEC.31: 20 residues within 4Å: Chain C: K.29, H.30, V.33, H.37, A.65, C.66, T.68, C.69, H.70, C.227, F.228, H.231, P.233, A.236 Chain D: H.37, T.68, C.69 Ligands: HEC.26, HEC.30, HEC.43 11 PLIP interactions: 1 interactions with chain D, 10 interactions with chain C, Water bridges: D:N.5, C:K.29 Hydrophobic interactions: C:K.29, C:K.29, C:V.33, C:T.68, C:H.231 Salt bridges: C:K.29, C:K.29 Metal complexes: C:H.30, C:H.70 HEC.32: 22 residues within 4Å: Chain C: V.9, Q.13, C.14, C.17, H.18, C.35, H.39, A.41, H.44, V.45, A.48, S.49, S.50, R.52, M.53, R.56, P.57, T.59, L.194, R.276, G.277 Ligands: HEC.30 14 PLIP interactions: 14 interactions with chain C, Hydrophobic interactions: C:V.9, C:A.41, C:V.45, C:M.53, C:P.57 Hydrogen bonds: C:G.277 Water bridges: C:R.276, C:R.276 Salt bridges: C:R.56, C:R.276, C:R.276 pi-Stacking: C:H.18 Metal complexes: C:H.18, C:H.44 HEC.37: 25 residues within 4Å: Chain D: H.113, A.114, E.115, P.116, D.125, H.126, V.129, R.131, A.179, A.180, C.184, C.187, K.188, R.242, Q.298, C.299, H.300, V.301, Y.303, C.305, F.327, H.361, N.486 Ligands: HEC.39, PO4.45 20 PLIP interactions: 20 interactions with chain D, Hydrophobic interactions: D:V.129, D:V.301, D:Y.303, D:Y.303, D:F.327 Hydrogen bonds: D:A.114, D:A.484, D:N.486 Water bridges: D:K.90, D:K.90, D:H.113, D:H.113, D:R.131 Salt bridges: D:K.90, D:H.113, D:R.131, D:H.361 pi-Stacking: D:Y.303, D:H.361 pi-Cation interactions: D:H.126 HEC.38: 20 residues within 4Å: Chain D: C.66, H.70, Q.73, F.74, F.77, L.225, N.226, C.227, M.229, C.230, H.231, A.290, S.292, M.295, M.384, Y.395, T.396, H.398 Ligands: HEC.39, HEC.43 11 PLIP interactions: 11 interactions with chain D, Hydrophobic interactions: D:H.70, D:Q.73, D:Q.73, D:L.225, D:A.290, D:T.396 Hydrogen bonds: D:Q.73, D:T.396 Salt bridges: D:K.386 Metal complexes: D:H.231, D:H.398 HEC.39: 27 residues within 4Å: Chain D: R.81, S.84, P.116, R.117, S.118, H.119, F.121, M.122, D.125, C.187, K.188, L.225, M.229, S.292, M.295, C.296, Q.298, C.299, H.300, C.379, H.383, M.384, Q.400, R.401 Ligands: HEC.37, HEC.38, HEC.40 12 PLIP interactions: 12 interactions with chain D, Hydrophobic interactions: D:P.116, D:K.188, D:L.225, D:H.383 Hydrogen bonds: D:R.117, D:F.121, D:D.125 Water bridges: D:S.84, D:H.126, D:Q.400 Metal complexes: D:H.119, D:H.300 HEC.40: 23 residues within 4Å: Chain D: N.293, C.296, H.300, E.363, A.364, F.367, H.372, V.377, A.378, C.379, C.382, H.383, T.402, P.403, R.404, I.427, K.431, N.486, S.487, F.490, H.491 Ligands: HEC.39, HEC.41 22 PLIP interactions: 22 interactions with chain D, Hydrophobic interactions: D:H.300, D:E.363, D:E.363, D:F.367, D:H.372, D:V.377, D:P.403, D:I.427, D:N.486, D:F.490, D:F.490 Hydrogen bonds: D:T.402, D:T.402 Water bridges: D:S.84, D:R.404, D:R.404, D:N.486, D:N.486 Salt bridges: D:R.404, D:K.431 Metal complexes: D:H.383, D:H.491 HEC.41: 20 residues within 4Å: Chain B: N.141, W.142, Q.143 Chain D: V.371, H.372, N.375, V.377, D.381, C.382, P.403, A.410, C.411, C.414, H.415, W.418, A.423, I.427, F.490, P.493 Ligands: HEC.40 13 PLIP interactions: 9 interactions with chain D, 4 interactions with chain B, Hydrophobic interactions: D:V.371, D:N.375, D:V.377, D:P.403, D:W.418, D:I.427, D:F.490, B:Q.143 Metal complexes: D:H.372, D:H.415 Hydrogen bonds: B:W.142, B:Q.143 Water bridges: B:Q.143 HEC.42: 24 residues within 4Å: Chain D: A.11, C.14, F.15, H.18, I.21, H.25, V.33, N.34, C.35, H.37, C.38, H.39, T.59, I.193, L.194, F.228, P.233, H.234, R.239, F.274, R.276, R.282 Ligands: HEC.43, HEC.44 18 PLIP interactions: 18 interactions with chain D, Hydrophobic interactions: D:A.11, D:F.15, D:I.21, D:I.21, D:V.33, D:T.59, D:I.193, D:L.194, D:F.228, D:P.233, D:F.274 Water bridges: D:H.234 Salt bridges: D:R.239, D:R.276, D:R.282, D:R.282 Metal complexes: D:H.39, D:H.234 HEC.43: 19 residues within 4Å: Chain C: H.37, T.68, C.69 Chain D: K.29, H.30, V.33, H.37, A.65, C.66, C.69, H.70, C.227, F.228, H.231, P.233, A.236 Ligands: HEC.31, HEC.38, HEC.42 7 PLIP interactions: 7 interactions with chain D, Hydrophobic interactions: D:K.29, D:V.33, D:H.231 Salt bridges: D:K.29, D:K.29 Metal complexes: D:H.30, D:H.70 HEC.44: 23 residues within 4Å: Chain D: Q.13, C.14, C.17, H.18, C.35, H.39, A.41, H.44, V.45, A.48, S.49, S.50, R.51, R.52, M.53, R.56, P.57, T.59, L.194, Q.275, R.276, G.277 Ligands: HEC.42 14 PLIP interactions: 14 interactions with chain D, Hydrophobic interactions: D:A.41, D:V.45, D:M.53, D:P.57 Water bridges: D:H.18, D:Q.275, D:R.276, D:R.276, D:R.278, D:R.278 Salt bridges: D:R.56, D:R.276 Metal complexes: D:H.18, D:H.44 HEC.49: 27 residues within 4Å: Chain E: H.113, A.114, E.115, P.116, D.125, H.126, V.129, R.131, A.132, A.179, A.180, C.184, C.187, K.188, R.242, Q.298, C.299, H.300, V.301, Y.303, C.305, F.327, H.361, A.484, N.486 Ligands: HEC.51, PO4.57 21 PLIP interactions: 21 interactions with chain E, Hydrophobic interactions: E:V.129, E:A.132, E:V.301, E:Y.303, E:Y.303, E:F.327 Hydrogen bonds: E:A.114, E:A.484, E:N.486 Water bridges: E:K.90, E:K.90, E:H.113, E:H.113, E:R.131 Salt bridges: E:K.90, E:H.113, E:R.131, E:H.361 pi-Stacking: E:Y.303, E:H.361 pi-Cation interactions: E:H.126 HEC.50: 21 residues within 4Å: Chain E: C.66, H.70, Q.73, F.74, F.77, L.225, N.226, C.227, M.229, C.230, H.231, A.290, S.292, M.295, M.384, K.386, Y.395, T.396, H.398 Ligands: HEC.51, HEC.55 12 PLIP interactions: 12 interactions with chain E, Hydrophobic interactions: E:H.70, E:Q.73, E:Q.73, E:L.225, E:A.290, E:T.396 Hydrogen bonds: E:Q.73, E:T.396, E:T.396 Salt bridges: E:K.386 Metal complexes: E:H.231, E:H.398 HEC.51: 26 residues within 4Å: Chain E: R.81, S.84, P.116, R.117, S.118, H.119, F.121, M.122, D.125, C.187, K.188, L.225, M.229, S.292, C.296, Q.298, C.299, H.300, C.379, H.383, M.384, Q.400, R.401 Ligands: HEC.49, HEC.50, HEC.52 10 PLIP interactions: 10 interactions with chain E, Hydrophobic interactions: E:P.116, E:L.225, E:H.383 Hydrogen bonds: E:S.84, E:P.116, E:R.117, E:S.118, E:F.121 Metal complexes: E:H.119, E:H.300 HEC.52: 24 residues within 4Å: Chain E: P.116, N.293, C.296, H.300, E.363, A.364, F.367, H.372, V.377, A.378, C.379, C.382, H.383, T.402, P.403, R.404, I.427, K.431, N.486, S.487, F.490, H.491 Ligands: HEC.51, HEC.53 21 PLIP interactions: 21 interactions with chain E, Hydrophobic interactions: E:H.300, E:E.363, E:E.363, E:F.367, E:H.372, E:V.377, E:P.403, E:I.427, E:N.486, E:F.490, E:F.490 Hydrogen bonds: E:T.402 Water bridges: E:S.84, E:R.404, E:R.404, E:N.486, E:N.486 Salt bridges: E:R.404, E:K.431 Metal complexes: E:H.383, E:H.491 HEC.53: 20 residues within 4Å: Chain A: N.141, W.142, Q.143 Chain E: V.371, H.372, N.375, V.377, D.381, C.382, P.403, A.410, C.411, C.414, H.415, W.418, A.423, I.427, F.490, P.493 Ligands: HEC.52 11 PLIP interactions: 8 interactions with chain E, 3 interactions with chain A, Hydrophobic interactions: E:V.371, E:V.377, E:P.403, E:W.418, E:I.427, E:F.490, A:Q.143 Metal complexes: E:H.372, E:H.415 Hydrogen bonds: A:W.142 Water bridges: A:Q.143 HEC.54: 23 residues within 4Å: Chain E: C.14, F.15, H.18, I.21, H.25, V.33, N.34, C.35, H.37, C.38, H.39, T.59, I.193, L.194, F.228, P.233, H.234, R.239, F.274, R.276, R.282 Ligands: HEC.55, HEC.56 17 PLIP interactions: 17 interactions with chain E, Hydrophobic interactions: E:F.15, E:I.21, E:V.33, E:T.59, E:I.193, E:L.194, E:F.228, E:P.233, E:P.233, E:F.274 Water bridges: E:H.234 Salt bridges: E:R.239, E:R.276, E:R.282, E:R.282 Metal complexes: E:H.39, E:H.234 HEC.55: 20 residues within 4Å: Chain E: K.29, H.30, V.33, H.37, A.65, C.66, T.68, C.69, H.70, C.227, F.228, H.231, P.233, A.236 Chain F: H.37, T.68, C.69 Ligands: HEC.50, HEC.54, HEC.67 12 PLIP interactions: 10 interactions with chain E, 2 interactions with chain F, Hydrophobic interactions: E:K.29, E:K.29, E:V.33, E:T.68, E:H.231 Water bridges: E:K.29, F:N.5, F:T.68 Salt bridges: E:K.29, E:K.29 Metal complexes: E:H.30, E:H.70 HEC.56: 22 residues within 4Å: Chain E: V.9, Q.13, C.14, C.17, H.18, C.35, H.39, A.41, H.44, V.45, A.48, S.49, S.50, R.52, M.53, R.56, P.57, T.59, L.194, R.276, G.277 Ligands: HEC.54 14 PLIP interactions: 14 interactions with chain E, Hydrophobic interactions: E:V.9, E:A.41, E:V.45, E:M.53, E:P.57 Hydrogen bonds: E:G.277 Water bridges: E:R.276, E:R.276 Salt bridges: E:R.56, E:R.276, E:R.276 pi-Stacking: E:H.18 Metal complexes: E:H.18, E:H.44 HEC.61: 25 residues within 4Å: Chain F: H.113, A.114, E.115, P.116, D.125, H.126, V.129, R.131, A.179, A.180, C.184, C.187, K.188, R.242, Q.298, C.299, H.300, V.301, Y.303, C.305, F.327, H.361, N.486 Ligands: HEC.63, PO4.69 20 PLIP interactions: 20 interactions with chain F, Hydrophobic interactions: F:V.129, F:V.301, F:Y.303, F:Y.303, F:F.327 Hydrogen bonds: F:A.114, F:A.484, F:N.486 Water bridges: F:K.90, F:K.90, F:H.113, F:H.113, F:R.131 Salt bridges: F:K.90, F:H.113, F:R.131, F:H.361 pi-Stacking: F:Y.303, F:H.361 pi-Cation interactions: F:H.126 HEC.62: 20 residues within 4Å: Chain F: C.66, H.70, Q.73, F.74, F.77, L.225, N.226, C.227, M.229, C.230, H.231, A.290, S.292, M.295, M.384, Y.395, T.396, H.398 Ligands: HEC.63, HEC.67 11 PLIP interactions: 11 interactions with chain F, Hydrophobic interactions: F:H.70, F:Q.73, F:Q.73, F:L.225, F:A.290, F:T.396 Hydrogen bonds: F:Q.73, F:T.396 Salt bridges: F:K.386 Metal complexes: F:H.231, F:H.398 HEC.63: 27 residues within 4Å: Chain F: R.81, S.84, P.116, R.117, S.118, H.119, F.121, M.122, D.125, C.187, K.188, L.225, M.229, S.292, M.295, C.296, Q.298, C.299, H.300, C.379, H.383, M.384, Q.400, R.401 Ligands: HEC.61, HEC.62, HEC.64 12 PLIP interactions: 12 interactions with chain F, Hydrophobic interactions: F:P.116, F:K.188, F:L.225, F:H.383 Hydrogen bonds: F:S.84, F:R.117, F:F.121, F:D.125 Water bridges: F:H.126, F:Q.400 Metal complexes: F:H.119, F:H.300 HEC.64: 23 residues within 4Å: Chain F: N.293, C.296, H.300, E.363, A.364, F.367, H.372, V.377, A.378, C.379, C.382, H.383, T.402, P.403, R.404, I.427, K.431, N.486, S.487, F.490, H.491 Ligands: HEC.63, HEC.65 22 PLIP interactions: 22 interactions with chain F, Hydrophobic interactions: F:H.300, F:E.363, F:E.363, F:F.367, F:H.372, F:V.377, F:P.403, F:I.427, F:N.486, F:F.490, F:F.490 Hydrogen bonds: F:T.402 Water bridges: F:S.84, F:R.404, F:R.404, F:K.431, F:N.486, F:N.486 Salt bridges: F:R.404, F:K.431 Metal complexes: F:H.383, F:H.491 HEC.65: 20 residues within 4Å: Chain D: N.141, W.142, Q.143 Chain F: V.371, H.372, N.375, V.377, D.381, C.382, P.403, A.410, C.411, C.414, H.415, W.418, A.423, I.427, F.490, P.493 Ligands: HEC.64 13 PLIP interactions: 9 interactions with chain F, 4 interactions with chain D, Hydrophobic interactions: F:V.371, F:N.375, F:V.377, F:P.403, F:W.418, F:I.427, F:F.490, D:Q.143 Metal complexes: F:H.372, F:H.415 Hydrogen bonds: D:W.142, D:Q.143 Water bridges: D:Q.143 HEC.66: 24 residues within 4Å: Chain F: A.11, C.14, F.15, H.18, I.21, H.25, V.33, N.34, C.35, H.37, C.38, H.39, T.59, I.193, L.194, F.228, P.233, H.234, R.239, F.274, R.276, R.282 Ligands: HEC.67, HEC.68 18 PLIP interactions: 18 interactions with chain F, Hydrophobic interactions: F:A.11, F:F.15, F:I.21, F:I.21, F:V.33, F:T.59, F:I.193, F:L.194, F:F.228, F:P.233, F:F.274 Water bridges: F:H.234 Salt bridges: F:R.239, F:R.276, F:R.282, F:R.282 Metal complexes: F:H.39, F:H.234 HEC.67: 19 residues within 4Å: Chain E: H.37, T.68, C.69 Chain F: K.29, H.30, V.33, H.37, A.65, C.66, C.69, H.70, C.227, F.228, H.231, P.233, A.236 Ligands: HEC.55, HEC.62, HEC.66 7 PLIP interactions: 7 interactions with chain F, Hydrophobic interactions: F:K.29, F:V.33, F:H.231 Salt bridges: F:K.29, F:K.29 Metal complexes: F:H.30, F:H.70 HEC.68: 23 residues within 4Å: Chain F: Q.13, C.14, C.17, H.18, C.35, H.39, A.41, H.44, V.45, A.48, S.49, S.50, R.51, R.52, M.53, R.56, P.57, T.59, L.194, Q.275, R.276, G.277 Ligands: HEC.66 14 PLIP interactions: 14 interactions with chain F, Hydrophobic interactions: F:A.41, F:V.45, F:M.53, F:P.57 Water bridges: F:H.18, F:Q.275, F:R.276, F:R.276, F:R.278, F:R.278 Salt bridges: F:R.56, F:R.276 Metal complexes: F:H.18, F:H.44

6 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.9: 8 residues within 4Å: Chain A: F.109, H.113, R.131, K.188, Y.303, Q.360, H.361 Ligands: HEC.1 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:Y.303, A:Q.360 Water bridges: A:H.113, A:R.131, A:R.131 Salt bridges: A:R.131, A:K.188, A:H.361 PO4.21: 8 residues within 4Å: Chain B: F.109, H.113, R.131, K.188, Y.303, Q.360, H.361 Ligands: HEC.13 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:Y.303, B:Y.303, B:Y.303 Water bridges: B:H.113, B:R.131, B:R.131 Salt bridges: B:R.131, B:K.188, B:H.361 PO4.33: 8 residues within 4Å: Chain C: F.109, H.113, R.131, K.188, Y.303, Q.360, H.361 Ligands: HEC.25 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:Y.303, C:Y.303, C:Y.303, C:Q.360 Water bridges: C:H.113, C:R.131, C:R.131 Salt bridges: C:R.131, C:K.188, C:H.361 PO4.45: 8 residues within 4Å: Chain D: F.109, H.113, R.131, K.188, Y.303, Q.360, H.361 Ligands: HEC.37 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:Y.303, D:Y.303, D:Q.360 Water bridges: D:H.113, D:R.131, D:R.131 Salt bridges: D:R.131, D:K.188, D:H.361 PO4.57: 8 residues within 4Å: Chain E: F.109, H.113, R.131, K.188, Y.303, Q.360, H.361 Ligands: HEC.49 7 PLIP interactions: 7 interactions with chain E Hydrogen bonds: E:Y.303 Water bridges: E:H.113, E:R.131, E:R.131 Salt bridges: E:R.131, E:K.188, E:H.361 PO4.69: 8 residues within 4Å: Chain F: F.109, H.113, R.131, K.188, Y.303, Q.360, H.361 Ligands: HEC.61 7 PLIP interactions: 7 interactions with chain F Hydrogen bonds: F:Y.303 Water bridges: F:H.113, F:R.131, F:R.131 Salt bridges: F:R.131, F:K.188, F:H.361

6 x CA: CALCIUM ION(Non-covalent)

CA.10: 6 residues within 4Å: Chain A: E.302, Y.303, F.328, K.358, L.359, Q.360 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.302, A:Y.303, A:K.358, H2O.12, H2O.12 CA.22: 6 residues within 4Å: Chain B: E.302, Y.303, F.328, K.358, L.359, Q.360 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.302, B:Y.303, B:K.358, H2O.33, H2O.33 CA.34: 6 residues within 4Å: Chain C: E.302, Y.303, F.328, K.358, L.359, Q.360 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.302, C:Y.303, C:K.358, H2O.52, H2O.52 CA.46: 6 residues within 4Å: Chain D: E.302, Y.303, F.328, K.358, L.359, Q.360 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.302, D:Y.303, D:K.358, H2O.73, H2O.73 CA.58: 6 residues within 4Å: Chain E: E.302, Y.303, F.328, K.358, L.359, Q.360 5 PLIP interactions: 3 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:E.302, E:Y.303, E:K.358, H2O.92, H2O.92 CA.70: 6 residues within 4Å: Chain F: E.302, Y.303, F.328, K.358, L.359, Q.360 5 PLIP interactions: 3 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:E.302, F:Y.303, F:K.358, H2O.113, H2O.113

9 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.11: 9 residues within 4Å: Chain A: R.87, V.128, Q.138, F.139, W.142, V.145 Chain E: Y.429, Y.433, R.497 8 PLIP interactions: 7 interactions with chain A, 1 interactions with chain E Hydrophobic interactions: A:F.139, A:W.142, A:W.142, A:V.145, E:Y.429 Hydrogen bonds: A:R.87, A:R.87, A:F.139 MPD.12: 4 residues within 4Å: Chain A: R.96, K.431, N.432, H.435 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:K.431, A:H.435 Hydrogen bonds: A:N.432 MPD.23: 9 residues within 4Å: Chain B: R.87, V.128, Q.138, F.139, W.142, V.145 Chain D: Y.429, Y.433, R.497 9 PLIP interactions: 7 interactions with chain B, 2 interactions with chain D Hydrophobic interactions: B:F.139, B:W.142, B:W.142, B:V.145, D:Y.429, D:Y.433 Hydrogen bonds: B:R.87, B:R.87, B:F.139 MPD.35: 9 residues within 4Å: Chain A: Y.429, Y.433, R.497 Chain C: R.87, V.128, Q.138, F.139, W.142, V.145 8 PLIP interactions: 7 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:F.139, C:W.142, C:W.142, C:V.145, A:Y.429 Hydrogen bonds: C:R.87, C:R.87, C:F.139 MPD.36: 4 residues within 4Å: Chain C: R.96, K.431, N.432, H.435 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:K.431, C:H.435 Hydrogen bonds: C:N.432 MPD.47: 9 residues within 4Å: Chain D: R.87, V.128, Q.138, F.139, W.142, V.145 Chain F: Y.429, Y.433, R.497 9 PLIP interactions: 7 interactions with chain D, 2 interactions with chain F Hydrophobic interactions: D:F.139, D:W.142, D:W.142, D:V.145, F:Y.429, F:Y.433 Hydrogen bonds: D:R.87, D:R.87, D:F.139 MPD.59: 9 residues within 4Å: Chain C: Y.429, Y.433, R.497 Chain E: R.87, V.128, Q.138, F.139, W.142, V.145 8 PLIP interactions: 7 interactions with chain E, 1 interactions with chain C Hydrophobic interactions: E:F.139, E:W.142, E:W.142, E:V.145, C:Y.429 Hydrogen bonds: E:R.87, E:R.87, E:F.139 MPD.60: 4 residues within 4Å: Chain E: R.96, K.431, N.432, H.435 3 PLIP interactions: 3 interactions with chain E Hydrophobic interactions: E:K.431, E:H.435 Hydrogen bonds: E:N.432 MPD.71: 9 residues within 4Å: Chain B: Y.429, Y.433, R.497 Chain F: R.87, V.128, Q.138, F.139, W.142, V.145 9 PLIP interactions: 7 interactions with chain F, 2 interactions with chain B Hydrophobic interactions: F:F.139, F:W.142, F:W.142, F:V.145, B:Y.429, B:Y.433 Hydrogen bonds: F:R.87, F:R.87, F:F.139

3 x MRD: (4R)-2-METHYLPENTANE-2,4-DIOL(Non-functional Binders)

MRD.24: 5 residues within 4Å: Chain B: S.95, R.96, K.431, N.432, H.435 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:H.435 Water bridges: B:N.432 MRD.48: 5 residues within 4Å: Chain D: S.95, R.96, K.431, N.432, H.435 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:H.435 Hydrogen bonds: D:K.431 Water bridges: D:N.432 MRD.72: 5 residues within 4Å: Chain F: S.95, R.96, K.431, N.432, H.435 3 PLIP interactions: 3 interactions with chain F Hydrophobic interactions: F:H.435 Hydrogen bonds: F:K.431 Water bridges: F:N.432

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Trofimov, A.A. et al., Structure of octaheme cytochrome c nitrite reductase from Thioalkalivibrio nitratireducens in a complex with phosphate. Crystallography Reports (2010)

Release Date

2009-08-04

Peptides

Eight-heme nitrite reductase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

E
A

F
B

Eight-heme nitrite reductase

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